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A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Human Virology and Viral Diseases".

Deadline for manuscript submissions: closed (31 October 2025) | Viewed by 11300

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Dr. Celso Cunha

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Guest Editor

Institute of Hygiene and Tropical Medicine, NOVA University, Lisbon, Portugal
Interests: rotavirus; hepatitis D virus; hepatitis B virus; virus–host interactions
Special Issues, Collections and Topics in MDPI journals

Dr. Claudia Istrate

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Guest Editor

Interdisciplinary Center for Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
Interests: rotavirus; norovirus; viruses causing gastroenteritis; African swine fever virus; vaccine development; molecular epidemiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

It is estimated that 50-70% of all cases of infectious acute gastroenteritis (AGE) worldwide are caused by viruses. Noroviruses, rotaviruses, adenoviruses and astroviruses are the main causative agents, accounting for 3-5 billion cases and 1.5 million deaths per year; these particularly affect children in low and middle-income countries (LMIC) with poor access to safe water, sanitation and health care infrastructure.

Prevention and vaccination remain the sole means of reducing the incidence of this disease. As of today, the only approved vaccines target rotaviruses, and these are included in infant vaccination plans in many countries, contributing to a reduction in the number of new infections and cases of severe diarrhea. However, these vaccines seem to show reduced efficacy in LMICs. Several factors might contribute to this phenomenon, including host genetic factors (e.g., histo-blood group antigens (HBGAs)), the gut microbiota and environmental enteropathy. Several vaccine candidates that target noroviruses are also being tested in clinical trials at different stages.

Rotaviruses, noroviruses and astroviruses have RNA genomes with significantly higher rates of mutation when compared to DNA viruses, including adenoviruses. Therefore, the implementation of monitoring plans that aim to control circulating strains and variants is crucial to ensuring the accuracy of laboratory diagnosis.

This Special Issue will focus on the mechanisms implicated in the pathogenesis of viruses associated with acute gastroenteritis, with an emphasis on their pathophysiology, virus tropism and replication, vaccine design and production, preventive measures, the development of new therapeutic approaches, the immune response, differential laboratory diagnosis, the role of the microbiota, host genetic factors, molecular epidemiology, and surveillance.

Dr. Celso Cunha
Dr. Claudia Istrate
Guest Editors

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Keywords

vaccines
therapeutic approaches
virus replication
molecular epidemiology
immune response
microbiome
diagnosis

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Viruses Associated with Gastroenteritis: 2nd Edition in Viruses

Published Papers (9 papers)

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Editorial

Jump to: Research, Other

3 pages, 157 KB

Open AccessEditorial

Special Issue: “Viruses Associated with Gastroenteritis”

by Celso Cunha and Claudia Istrate

Viruses 2026, 18(1), 22; https://doi.org/10.3390/v18010022 - 23 Dec 2025

Abstract

Diarrheal diseases are the third leading cause of death in children under 5 years of age, with approximately 450 [...] Full article

(This article belongs to the Special Issue Viruses Associated with Gastroenteritis)

Research

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11 pages, 830 KB

Open AccessArticle

Trends in Norovirus Genotypes in South Korea, 2019–2024: Insights from Nationwide Dual Typing Surveillance

by Minji Lee, Seung-Rye Cho, Yunhee Jo, Deog-Yong Lee, Myung-Guk Han and Sun-Whan Park

Viruses 2025, 17(12), 1572; https://doi.org/10.3390/v17121572 - 30 Nov 2025

Viewed by 790

Abstract

Noroviruses are a leading cause of acute gastroenteritis worldwide, with a particularly high burden among children under five years of age. We analyzed nationwide surveillance data from EnterNet-Korea collected between 2019 and 2024—covering both the pre- and post-COVID-19 pandemic periods—to assess norovirus detection rates and genotype distribution. Noroviruses were detected by RT-qPCR, and dual genotyping of capsid (G) and polymerase (P) types was performed by sequencing the ORF1–2 junction region. Among the 67,159 specimens tested, 8.4% (n = 5652) were norovirus-positive, with the highest prevalence observed in children aged 0–5 years (19.9%). In this age group, genotyping was successful in 72.4% (2633/3635) of positive cases, identifying 30 distinct genotypes (GI: 9; GII: 21). The most common strains were GII.4[P31] (38.1%), GII.4[P16] (27.1%), and GII.2[P16] (10.4%), with substantial year-to-year variation. Notably, the emergence of GII.17[P17] in late 2024 indicates shifting genotype dynamics, underscoring the need for strengthened surveillance and reconsideration of vaccine strain selection. To our knowledge, this is the first nationwide dual-typing study in Korea encompassing the COVID-19 pandemic era. These findings provide essential baseline data for integration into global surveillance systems and inform future vaccine development and public health strategies. Full article

(This article belongs to the Special Issue Viruses Associated with Gastroenteritis)

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29 pages, 6741 KB

Open AccessArticle

Unveiling the Genomic Landscape of G2P[6] Rotavirus a Strains in Brazil: Evolutionary and Epidemiological Perspectives

by Vanessa Cristina Martins Silva, Yasmin França, Lais Sampaio de Azevedo, Raquel Guiducci, Edlaine Faria de Moura Villela and Adriana Luchs

Viruses 2025, 17(8), 1103; https://doi.org/10.3390/v17081103 - 11 Aug 2025

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Abstract

In Brazil, molecular surveillance expanded after Rotarix™ vaccine introduction, alongside G2P[4] dominance. The G2P[6] genotype, despite sharing the same DS-1-like constellation as G2P[4] strains, remains rare. This retrospective study analyzed eight Brazilian G2P[6] strains (2012–2014) through RT-PCR and 11-segments sequencing, followed by phylogenetic analysis. Two distinct groups were identified: 2012–2013 strains (six) carried a DS-1-like backbone with the rare NSP4 E6 genotype, while 2014 strains (two) exhibited the classical DS-1-like constellation with E2. Phylogenetic analysis confirmed the two main clusters: 2012–2013 strains related to classical G2P[4] and uncommon global genotypes, and 2014 strains resembling emerging DS-1-like G1/G3/G8P[8] reassortants. The 2012–2013 strains clustered within G2-VP7 Lineage IVa, while the 2014 strains belonged to Lineage V, reflecting the global distribution of these variants. All VP4 genes were classified within the P[6]-Ia lineage, with phylogenetic analyses suggesting separate introductions from Asia and Africa. The E6 NSP4 gene segment identified in these strains has an undetermined origin and was not previously associated with G2P[6] strains in Brazil. Despite similarities to G2P[4], G2P[6] strains remain rare, with no genomic features explaining their limited spread. Phylogenetic data indicate multiple reassortment events and international viral exchange, highlighting Brazil’s role in RVA diversity. Ongoing full-genome surveillance is crucial to track rare variants and assess their public health relevance. Full article

(This article belongs to the Special Issue Viruses Associated with Gastroenteritis)

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19 pages, 1819 KB

Open AccessArticle

Rotavirus alphagastroenteritidis: Circulating Strains After the Introduction of the Rotavirus Vaccine (Rotarix^®) in Luanda Province of Angola

by Dikudila G. Vita, Cristina Santiso-Bellón, Manuel Lemos, Zoraima Neto, Elsa Fortes-Gabriel, Miguel Brito, Cruz S. Sebastião, Jesus Rodriguez-Diaz, Celso Cunha and Claudia Istrate

Viruses 2025, 17(6), 858; https://doi.org/10.3390/v17060858 - 17 Jun 2025

Cited by 1 | Viewed by 1555

Abstract

Rotavirus alphagastroenteritidis (R. alphagastroenteritidis) remains the leading cause of pediatric diarrhea. Although Angola introduced Rotarix^®, the human monovalent R. alphagastroenteritidis vaccine since 2014 as part of its routine childhood immunization program, no follow-up study has been conducted. The aim of this study was to evaluate the distribution of R. alphagastroenteritidis genotypes among children under five years of age, hospitalized with acute gastroenteritis (AGE), after the introduction of the rotavirus vaccine. To achieve this goal, stool samples collected between 2021 and 2022 from children under 5 years of age diagnosed with AGE at six hospitals in Luanda Province were analyzed. The R. alphagastroenteritidis-antigen immunochromatographic test (SD Bioline™, Abbott, Chicago, IL, USA) was performed, and 121 positive samples were genotyped. Ten samples were randomly selected for further Sanger sequencing. The results showed that the G9P[6] was the most prevalent genotype (17.3%), followed by G9P[8] (16.5%), G2P[4] (14.9%), G3P[6] (13.2%), G8P[6] (11.5%), and less frequently G12P[8] (9.1%), G1P[6] (4.1%), and G1P[8] (2.5%). The genotype combinations G3P[6], G8P[6], and G12P[8] were detected for the first time in Luanda Province. In conclusion, the emergence of new genotype combinations supports the need for continuous surveillance to identify the trend in R. alphagastroenteritidis infection and the emergence of new strains circulating in Luanda Province in the post-vaccination period. Full article

(This article belongs to the Special Issue Viruses Associated with Gastroenteritis)

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19 pages, 3132 KB

Open AccessArticle

Molecular Epidemiology of Human Adenovirus from Acute Gastroenteritis Cases in Brazil After the COVID-19 Pandemic Period, 2021–2023

by Mateus de Souza Mello, Fábio Correia Malta, Alexandre Madi Fialho, Fernanda Marcicano Burlandy and Tulio Machado Fumian

Viruses 2025, 17(4), 577; https://doi.org/10.3390/v17040577 - 17 Apr 2025

Cited by 3 | Viewed by 3046

Abstract

Human enteric adenoviruses (HAdV-F40/41) play a crucial role as causative agents of acute gastroenteritis (AGE), particularly affecting children in low-and middle-income countries. This study investigated the prevalence, genetic diversity, and molecular characteristics of HAdV-F40/41 in AGE cases reported in Brazil from 2021 to 2023, a period after the COVID-19 pandemic. A total of 1980 stool samples collected from medically attended AGE patients from nine states were analyzed by TaqMan-based qPCR. Overall, HAdV was detected in 16.6% (n = 328/1980) of cases, with the highest prevalence observed in children under five years of age. The positive HAdV samples were genotyped through partial sequencing of the hexon and/or fiber genes followed by phylogenetic analysis. Enteric HAdVs (HAdV-F40/41) were detected in 3.2% (n = 63/1980) of samples, with HAdV-F41 (44.1%) being the most common genotype. Among the non-enteric types, HAdV-C (29.4%) was the most prevalent, followed by HAdV-B (13.2%), HAdV-A (10.3%), and HAdV-D (2.9%). Phylogenetic analysis of the hexon (HVR1–HVR6) and fiber (Shaft) gene regions identified two major clusters, H-GTC1 and F-GTC2, showing close genetic relationships with global strains. HAdV-F40/41 demonstrated significantly higher viral loads compared to non-enteric HAdVs. These findings highlight the importance of continued surveillance of HAdV-F to better understand its role in AGE cases and support public health strategies, including potential vaccine development. Full article

(This article belongs to the Special Issue Viruses Associated with Gastroenteritis)

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16 pages, 2720 KB

Open AccessArticle

Concurrent Circulation of Viral Agents in Pediatric Patients Presenting with Respiratory Illness and Diarrheal Symptoms in Metropolitan Region of São Paulo, Brazil, 2021

by Adriana Luchs, Natanael Sutikno Adiwardana, Leonardo Cecilio da Rocha, Ellen Viana, Simone Guadagnucci, Adriana Parise, Vanessa Cristina Martins Silva, Lais Sampaio de Azevedo, Raquel Guiducci, Yasmin França, Natacha Luana Pezzuol Frank, Ana Lucia Nascimento da Silva, Andre Luiz Vianna de Oliveira, André Henrique Souza Azevedo, Bárbara Segatelli Carreteiro and Maurício Lacerda Nogueira

Viruses 2025, 17(4), 497; https://doi.org/10.3390/v17040497 - 29 Mar 2025

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Abstract

Pneumonia and diarrhea are the leading causes of death in children under 5 globally, worsened by viral infections. This study investigates viral agents in children ≤ 3 years with respiratory illness and diarrhea in Metropolitan Region of São Paulo, Brazil, during spring 2021. Twenty paired samples (oropharyngeal swab and feces) were tested using in-house qPCR for HBoV and HAdV, RT-qPCR for RVA, EV, PeV-A, and NoV, and a commercial RT-qPCR kit for SARS-CoV-2, Flu A/B, and RSV. HAstV was detected with conventional nested (RT)-PCR. Positive samples were sequenced for molecular characterization and phylogenetic analysis. Seven viruses were identified: HBoV, NoV, HAdV, PeV-A, EV, RSV, and Flu A. HBoV and NoV were detected in 75% of cases, with co-infection in 65% of patients, indicating their involvement in the gastro-respiratory illness. Genotyping of HBoV (HBoV-1), NoV (GII.4_Sydney[P16], GII.2[P16], and GII.4_Sydney[P31]), EV (Coxsackievirus A6), HAdV (species C, type 6), and PeV-A (genotype 1) showed local virus diversity. Phylogenetic analysis indicated no ongoing community outbreak, with distinct clusters observed. The findings highlight the overlap of respiratory and enteric diseases, revealing local viral diversity and high exposure to enteric viruses. This underscores the challenges in differential diagnosis and the need for syndromic surveillance. Full article

(This article belongs to the Special Issue Viruses Associated with Gastroenteritis)

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11 pages, 1450 KB

Open AccessArticle

Epidemiological and Genetic Characteristics of Sapovirus in Shandong, China, 2022–2023

by Mingxin Guo, Meijia Li, Ti Liu, Wenkui Sun, Kaige Du, Shuopeng Yang, Zhongyan Fu and Zengqiang Kou

Viruses 2025, 17(4), 469; https://doi.org/10.3390/v17040469 - 26 Mar 2025

Cited by 1 | Viewed by 902

Abstract

Sapovirus (SaV) is a major pathogen responsible for acute gastroenteritis (AGE), and its incidence has been increasing in recent years. This study investigates the prevalence and the genetic characteristics of SaV in Shandong Province during 2022–2023, based on a surveillance network covering all age groups. Samples were obtained from a viral diarrhea surveillance network in Shandong Province during 2022–2023. SaVs were identified through quantitative reverse-transcription polymerase chain reaction (RT-qPCR). PCR amplification and Sanger sequencing were performed on positive samples, and whole-genome sequencing was conducted using metagenomic sequencing technology. Sequence analysis was conducted using BioEdit 7.0.9.0 and MEGA X, while statistical analysis was performed with SPSS 26.0. A total of 157 SaV-positive cases were identified, resulting in a positivity rate of 1.12%. The positivity rate for SaV was 0.75% in 2022 and it increased significantly to 1.42% in 2023. The highest positivity rates for both 2022 and 2023 were observed in November. The highest positivity rate was observed in the 3–5-year-old age group. In 2022, Dongying City had the highest positivity rate, while Zaozhuang City exhibited the highest rate in 2023. The incidence of vomiting in SaV-positive patients was significantly higher compared to SaV-negative patients (P = 0.002). Eight genotypes were identified in both the VP1 and RdRp regions. The complete genome sequence analysis of a GI.3 strain showed that NS1 (5.88%, 4/68) was the region most prone to amino acid variation, followed by VP2 (5.45%, 9/165) within the same genotype. SaV infections are more prevalent in cold weather, with young children being particularly susceptible. The SaV positivity rate in 2023 increased significantly accompanied by an increased diversity of genotypes, compared to that of 2022. The NS1 region exhibits the biggest variation within the same genotype, indicating that more attention should be paid to other regions besides VP1 in the future study. Ongoing surveillance of SaV is recommended for effective prevention and control. Full article

(This article belongs to the Special Issue Viruses Associated with Gastroenteritis)

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12 pages, 1230 KB

Open AccessArticle

Significant Association Between Increased Abundance of Selected Bacterial Lipopolysaccharides and Norovirus Diarrhea Among South African Infants

by Lerato P. Kgosana, Mapaseka L. Seheri and Cliff A. Magwira

Viruses 2025, 17(2), 278; https://doi.org/10.3390/v17020278 - 17 Feb 2025

Viewed by 1194

Abstract

Bacterial lipopolysaccharides (LPS) have been shown to promote enteric viral infections. This study assessed whether possessing elevated levels of LPS was associated with norovirus infection. Fecal samples from diarrheic norovirus-positive (DNP) (n = 26), non-diarrheal norovirus-negative (NDNN) (n = 26), asymptomatic norovirus-positive (ANP) (n = 15), and diarrheic norovirus-negative (DNN) (n =15) infants were assayed for selected bacterial LPS by quantitative PCR. The mean levels of selected LPS gene targets were significantly high in DNP infants (6.17 ± 2.14 CFU/g) versus NDNN infants (4.13 ± 2.25 CFU/g), p = 0.003. So too was the abundance between DNP and DNN infants (p = 0.0023). The levels of selected LPS gene targets were high regardless of whether the infection was symptomatic or asymptomatic, p = 0.3808. The average expression of genes coding for selected LPS and their signalling molecule, Toll-like receptor 4 (TLR4), increased 7- and 2.5-fold, respectively, in DNP versus NDNN children. Infants possessing elevated levels of selected LPS-rich bacteria were 1.51 times more likely to develop norovirus diarrhea (95% CI: 1.14–2.01, p = 0.004). In conclusion, norovirus infection was associated with abundance of selected bacterial LPS, suggesting a possible role of bacterial LPS in norovirus infection. Full article

(This article belongs to the Special Issue Viruses Associated with Gastroenteritis)

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9 pages, 7115 KB

Open AccessBrief Report

Delayed Emergence of Norovirus GII.17 in Finland: Foodborne Outbreaks Reported During the 2024/25 Season

by Haider Al-Hello, Ruska Rimhanen-Finne and Carita Savolainen-Kopra

Viruses 2025, 17(12), 1530; https://doi.org/10.3390/v17121530 - 21 Nov 2025

Viewed by 899

Abstract

During the 2024/25 season, Finland experienced a delayed emergence of norovirus genotype GII.17, which had already become prevalent in several European countries and the United States during the previous season, 2023/24. In Finland, GII.17 was confirmed in three foodborne outbreaks and five sporadic cases, marking the highest number of detections to date. These cases were geographically distributed across southern, western, and northern Finland, indicating widespread circulation. Retrospective analysis of national surveillance data from 2014 to 2025 revealed that GII.17 had been detected sporadically in earlier years but never at this scale. The emergence of GII.17 coincided with a continued presence of GII.4 [P16], the previously dominant genotype. Phylogenetic analysis showed that Finnish GII.17 strains clustered with recent international strains, suggesting introduction from abroad. The findings highlight the importance of sustained genotyping and international surveillance to detect emerging norovirus variants and inform public health preparedness in Finland. Full article

(This article belongs to the Special Issue Viruses Associated with Gastroenteritis)

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